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index.Rmd
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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: false
editor_options:
chunk_output_type: console
---
I am interesting in understanding differential APA between human and chimpanzees. I used 3' Seq to identify PAS for total and nuclear frations of LCL in both species.
Preparation and QC:
* [Prepare annotation files for mapping ](annotationInfo.html)
* [Mapping statistics and plots](mapStats.html)
* [Liftover PAS](liftoverPAS.html)
* [Annotated PAS and make APA phenotype](annotatePAS.html)
* [Compare identified PAS with apaQTL PAS](comp2apaQTLPAS.html)
* [PCA plot to look at variation in data](NromalizePhenos.html)
* [Total Fraction](NormalizePheno_total.html)
* [Total Fraction- Prenormalized](NonNormPheno_total.html)
* [Nuclear Fraction](NormalizePheno_nuclear.html)
* [Correlation between individuals](CorrbetweenInd.html)
* [Verify sample identity](verifyBAM.Rmd)
* [3' Seq enrichement along gene bodies](EnrichmentEndofGenes.html)
Catalog PAS:
* [Number of PAS in each species](PASnumperSpecies.html)
Differential Isoform Analysis:
* [Human Total vs Nuclear Analysis](Human_TvN.html)
* [Chimp Total vs Nuclear Analysis](Chimp_TvN.html)
* [Nuclear Human vs. Chimp Analysis](Nuclear_HvC.html)
Quantify Phenotypes with RNA:
* [Differnetial Splicing](diffSplicing.html)
* [Differential Expression](diffExpression.html)
* [Differential Expression without bad samples](diffExpressionRemove2.html)
Extra QC and Analysis
* [Investigate bad RNA seq samples](InvestigateBadSamples.html)
* [Map RNA to hg19](MapRNAhg19.html)